R: One Health VBD Hub

# One Health VBD Hub

## Documentation for package ‘ohvbd’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

ad_basereq | Generate a base request string for the AREAdata database
assoc_ad | Associate other data sources with AREAdata data
assoc_gadm | Associate other data sources with gadm IDs
check_db_status | Check whether databases are currently online
check_ohvbd_config | Print current ohvbd configuration variables
clean_ad_cache | Delete all rda files from ohvbd AREAdata cache (Deprecated)
clean_ohvbd_cache | Delete files from ohvbd cache directories
extract | Extract specified data from a set of responses (Deprecated)
fetch | Fetch specified data from a set of ids
fetch_ad | Fetch AREAdata dataset
fetch_citations | Try to find the relevant citations for a dataset
fetch_citations_vd | Retrieve citations for vecdyn data
fetch_citations_vt | Retrieve citations for vectraits data
fetch_gadm_sfs | Fetch gadm mapping shapefiles
fetch_gbif | Fetch GBIF dataset/s by ID
fetch_glean_vd_chunked | Fetch and parse multiple VecDyn datasets by ID in chunks
fetch_glean_vt_chunked | Get and parse multiple VecTraits datasets by ID in chunks
fetch_vd | Fetch VecDyn dataset/s by ID
fetch_vd_counts | Fetch VecDyn dataset length by ID
fetch_vd_meta | Fetch VecDyn metadata table
fetch_vt | Fetch VecTraits dataset/s by ID
filter_db | Filter hub search results by database
find_vd_columns | Get current columns in VecDyn datasets
find_vd_ids | Get current IDs in VecDyn
find_vt_ids | Get current IDs in VecTraits
force_db | Force an object to appear to come from a specific database
format_time_overlap_bar | Format and print date overlaps
generate_vt_template | Generate a vectraits template from a short set of survey responses
get_default_ohvbd_cache | Get ohvbd cache locations
glean | Extract specified data from a set of responses
glean_ad | Extract data from AREAdata datasets
glean_gbif | Parse data from requests to GBIF
glean_vd | Parse data from requests to VecDyn
glean_vt | Parse data from requests to VecTraits
has_db | Test whether an object has provenance information
is_cached | Check whether an object has been loaded from cache by ohvbd
is_from | Test whether an object is considered to be from a particular database
list_ohvbd_cache | List all ohvbd cached files
match_countries | Match country names to their equivalent naturalearth WKT polygons
match_species | Match species names to their GBIF backbone ids
ohvbd.ids | Create a new ohvbd ID vector
ohvbd_attrs | Internal attributes
ohvbd_db | Database provenance
ohvbd_db<- | Database provenance
ohvbd_dryrun | Option: dry runs of ohvbd searches
search_hub | Search vbdhub.org
search_vd | Search VecDyn by keyword
search_vd_smart | Search VecDyn using the explorer's filters
search_vt | Search VecTraits by keyword
search_vt_smart | Search VecTraits using the explorer's filters
set_default_ohvbd_cache | Set the default ohvbd cache location
set_ohvbd_compat | Set ohvbd compatability mode to TRUE
tee | Tee a pipeline to extract the data at a given point
vb_basereq | Generate a base request object for the vectorbyte databases